Next Article in Journal
Comparative Analysis of Genome Wide DNA Methylation Profiles for the Genic Male Sterile Cabbage Line 01-20S and Its Maintainer Line
Previous Article in Journal
An ‛Aukward’ Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks
Article Menu
Issue 6 (June) cover image

Export Article

Open AccessCommunication
Genes 2017, 8(6), 163; doi:10.3390/genes8060163

Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses

1
College of Life Sciences, Nankai University, Tianjin 300071, China
2
State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou 730046, Gansu, China
3
U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA
4
School of Mathematical Sciences, Nankai University, Tianjin 300071, China
5
International Potato Center (CIP), Apartado 1558, Lima 12, Peru
6
Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Bin Yu
Received: 20 April 2017 / Revised: 26 May 2017 / Accepted: 12 June 2017 / Published: 16 June 2017
(This article belongs to the Section Plant Genetics and Genomics)
View Full-Text   |   Download PDF [1398 KB, uploaded 16 June 2017]   |  

Abstract

Small interfering RNA (siRNA) duplexes are short (usually 21 to 24 bp) double-stranded RNAs (dsRNAs) with several overhanging nucleotides at both 5′- and 3′-ends. It has been found that siRNA duplexes bind the RNA-induced silencing complex (RISC) and cleave the sense strands with endonucleases. In this study, for the first time, we detected siRNA duplexes induced by plant viruses on a large scale using next-generation sequencing (NGS) data. In addition, we used the detected 21 nucleotide (nt) siRNA duplexes with 2 nt overhangs to construct a dataset for future data mining. The analytical results of the features in the detected siRNA duplexes were consistent with those from previous studies. The investigation of siRNA duplexes is useful for a better understanding of the RNA interference (RNAi) mechanism. It can also help to improve the virus detection based on the small RNA sequencing (sRNA-seq) technologies and to rationally design siRNAs for RNAi experiments. View Full-Text
Keywords: siRNA duplex; RNAi; plant virus; small RNA-seq; virus detection siRNA duplex; RNAi; plant virus; small RNA-seq; virus detection
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Niu, X.; Sun, Y.; Chen, Z.; Li, R.; Padmanabhan, C.; Ruan, J.; Kreuze, J.F.; Ling, K.; Fei, Z.; Gao, S. Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses. Genes 2017, 8, 163.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Genes EISSN 2073-4425 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top